The aim of this study was to compare the digestion of milk proteins from deer and cow milk using in vitro digestion and to quantify the production of peptides using the O-phthaldialdehyde assay. Deer milk contained on average 8.8 ± 0.13% protein which is twice the levels found in cow milk (4.1 ± 0.02%). Deer and cow milk were digested in two steps; imitating both the human stomach (Pepsin, pH 2.5, 30 min) and the duodenum (Corolase PP, pH 7.5, 30 min). The degradation patterns of the milk proteins were visualized by SDS-PAGE and quantified using ImageJ software. Peptide production was significantly higher in deer milk than cow milk (P< 0.05). The commercial proteolytic enzymes degraded milk protein from deer more rapidly than those from cow. Deer casein was completely digested at 40 min of digestion (10 min into duodenum digestion) where as 14% of the casein was still present in cow milk. The digestibility of α-lactalbumin and immunoglobulin were also higher in deer milk than cow milk. However, β-lactoglobulin from both species appeared to be resistant to both gastric and duodenal digestion. This study shows that deer milk proteins were more digestible and produced more peptides than protein from cow milk. The bioactive functions of deer peptides are currently under investigation.